================================================================================
DATASET VERSION 3
Title: Data for "A Computational Quantum Model for Periodontal Low‑Level Laser Therapy: Analytical Prediction of Coherence and Excitation" (Revised Manuscript)
DOI: [Will be assigned upon upload]
Repository: https://doi.org/10.7910/DVN/THCRB2
================================================================================

DESCRIPTION:
This is Version 3 of the dataset accompanying the revised manuscript. It contains the corrected analytical results, simulation data, and reproducible code implementing the extended quantum model with separate relaxation (γ₁) and dephasing (γ_φ) rates.

CHANGES FROM VERSION 2:
1. Model extended to include separate collapse operators for relaxation (γ₁) and pure dephasing (γ_φ)
2. Coherence lifetime corrected to τ = 1/γ₂ where γ₂ = γ₁/2 + γ_φ
3. Quantum jump rate J = γ₁P_e included as physically relevant excitation flux
4. Rabi frequency estimates qualified with orientation averaging considerations
5. Invalid coherence amplitude A = Ω/(2γ) removed from all analyses
6. All figures regenerated with corrected parameters
7. Abstract and manuscript text revised to reflect corrected model

FILES INCLUDED:
1. corrected_model.py          - Main implementation of extended Lindblad model
2. generate_figures.py         - Code to regenerate Figures 1 and 2
3. calculate_tables.py         - Code to calculate Tables 1 and 2
4. reproduce_all_analysis.py   - Single script to reproduce all results
5. requirements.txt            - Python package dependencies
6. table1_data.csv             - Data for Table 1 (steady-state populations)
7. table2_data.csv             - Data for Table 2 (coherence lifetimes)
8. figure1_data.csv            - Time-series data for Figure 1
9. figure2_data.csv            - Time-series data for Figure 2
10. final_abstract.txt         - Corrected abstract from revised manuscript
11. revised_parameters.txt     - Detailed parameter explanations and justifications

MODEL PARAMETERS:
Characteristic rate: Γ = 1 MHz (unit conversion only)
Rabi frequencies: Ω/Γ = 0.05, 0.10, 0.20, 0.50
Relaxation rate: γ₁/Γ = 0.001 (fixed)
Dephasing rates: γ_φ/Γ = 0.05, 0.10, 0.20
Coherence lifetime: τ = 1/(γ₁/2 + γ_φ)

DEPENDENCIES:
Python 3.8+
QuTiP 4.7+
NumPy 1.21+
Matplotlib 3.5+
SciPy 1.7+

REPRODUCTION INSTRUCTIONS:
1. Install required packages: pip install -r requirements.txt
2. Run the complete analysis: python reproduce_all_analysis.py
3. Or run individual scripts in order:
   - python corrected_model.py
   - python calculate_tables.py
   - python generate_figures.py

CITATION:
When using this dataset, please cite both the original article and this dataset version:

[Authors]. (2024). A Computational Quantum Model for Periodontal Low‑Level Laser Therapy: Analytical Prediction of Coherence and Excitation. [Journal Name]. DOI: [Journal DOI]

[Authors]. (2024). Data for "A Computational Quantum Model for Periodontal Low‑Level Laser Therapy" - Version 3. Harvard Dataverse. https://doi.org/10.7910/DVN/THCRB2

LICENSE:
All files in this dataset are licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license.

CONTACT:
For questions about this dataset, please contact: [Your Email]

================================================================================
UPLOAD DATE: [Current Date]
VERSION: 3.0
================================================================================